We describe a highly selective and sensitive method for determination of estrone (E1) and beta-estradiol (E2) in sediments, using high-performance liquid chromatography/time-of-flight (HPLC-ToF) mass spectrometry. The method involved sequential cleanup of sediment extracts over solid phase extraction cartridges, normal phase HPLC, and immunoaffinity extraction, which combine to remove coeluting matrix interferences. Resulting method detection limits (0.03 and 0.04 ng/g for E1 and E2, respectively) are sufficient to determine E1 and E2 in estuarine sediments collected from sewage-impacted Jamaica Bay (New York, NY, USA). The ToF analyzer has a higher resolution (>6,000) than quadrupole mass analyzers and can provide accurate mass estimation to within 2 mDa, which helped in distinguishing steroids from isobaric matrix interferences. The E1 and E2 were internally mass calibrated with respect to their coeluting surrogate standards, and the mass measurement error was between 1.1 and 1.4 mDa. The levels of E1 and E2 ranged between 0.07 to 2.52 and 0.05 to 0.53 ng/g, respectively. The measured concentrations of steroids in sediments correlated closely with other wastewater tracers. Despite the low concentrations of sediment-associated estrogens, their predicted estrogenic potency exceeds that of other measured estrogenic contaminants.